In the conventional manufacturing process (e.g., Silicon-On-Insulator, SOI), the manufacturing of the trench isolation structure typically chooses a tetraethyl orthosilicate (TEOS) layer as the etching hardmask. When such a method is employed to manufacture the trench isolation structure, the wet-etching is at a relatively large scale, a relatively large groove will be formed in the top of the trench, the flatness is unfavorable and the structure is vulnerable to the polysilicon residue problem causing a soft connection which affects the performance of the product. In addition, the trench isolation structure obtained by such a method is of a relatively large critical dimension.